This is my first post on this forum and I would have to say that the amount of information available and code examples for the Arduino is very impressive.At my work place we have several small projects that use the ATmega1280 microcontrollers. Is is possible to burn the arduino bootloader into this micro using only the AVR JTAGICE mkII? I have seen bits of information that use the 'Burn Bootloader' option using the Arduino software but I'm still not clear. It would be nice if it is as simple as loading the hex file into it and setting the fuse bits.

Well it should be that simple. The 1280 bootloader hex file is located it the Arduino core folder calledATmegaBOOT_168_atmega1280.hex . And the fuse settings are located in the 1280 section of the boards.txt file also in the arduino core directory.